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I have an Amazon Kindle Keyboard, an iPhone, and an iPad.
I have purchased a load of eBooks from the publisher, O'Reilly, and have downloaded them on to the Kindle via USB.
I note these do not show up in my Kindle account on the Amazon website, and nor do they show up on my iPhone's or iPad's Kindle apps.
Is it possible to put non-Amazon eBook purchases into my Kindle account so they show up on all my devices?
You can do this depending on the file type. Install Amazon's Send to Kindle for Mac. It's a free app that lets you send your personal documents to your Kindle devices and Kindle iOS reading apps from your Mac.
You can send using drag and drop, or from the Finder, or from other Mac apps via the "Send to Kindle" option in the Print menu. You can also choose which devices and apps you want to send to.
The documents you send must be one of these file types:
If your file doesn't meet these requirements, you can always use a tool like Calibre to convert it to a compatible type.
When uploading .MOBI eBooks these need to be DRM free.
There's more info on using the app on Amazon's site.
I purchased an ebook in Mobi format from a seller other than Amazon. I used the Send to Kindle application on my PC to send it to my Kindle device (strangely, by Kindle for PC was not on the list of options - more on this later). It was delivered to my device right away, and I happily read it. I made many highlights (as I often do), and I wanted to see those highlights on my PC to prepare some teaching notes. However, I discovered that the book did not appear on my Kindle for PC. I also checked my history of highlights at https://kindle.amazon.com/your_highlights and they were not there either. I started to worry at this point, thinking that I only ever have access to my highlights on the Kindle device itself.
I called Amazon support and here's what we learned: we went to Manage Your Content and Devices and clicked on YOur Content. The book did not appear under books, but DID appear under Docs. I then clicked on the action button next to my book and clicked the Deliver to: Others link. This brought up a window with a drop-down list of all my devices - except my Kindle for PC or the Amazon Cloud Reader were greyed out. I picked my iPhone, and sure enough the book appeared there with my highlights (yay!). I then went to my iPad (without sending the book there explicitly) and it was there with my highlights again.
Short version: If you send a third-party mobi book to your kindle, it will sync between Kindle apps, but only if they are on a Kindle, iOS or Android device; the cloud reader and PC applications (maybe Mac, too?) will not have the book or its associated notes/highlights.
An excellent way to do this besides the Send To Kindle app is to use your Send To Kindle email address which allows you to send all kinds of files directly to a Kindle device or device running an Kindle app. The best thing to do is to send it to your Kindle cloud account, which has 5 GBS of free space, and from there you can just download to any device using the Cloud tab. To get more info on how to find your email addresses and all that check out this link http://www.amazon.com/gp/sendtokindle/email
It seems Kindle exclusively supports purchased ebook sync as Amazon won't auto sync every sideloaded book. Things are quite different on iPad and iPhone as iBooks supports purchased & non-purchased book sync. However, you must hope to sync between your Kindle and apple device.
Here is a guide exactly concerning how to sync the furthest page among various OS & devices, which does not suit you well but might be of help more or less.
